By Dr David Samuel Khoury

Preprints

Stadler E; Khan SR; Elias KM; Egilmezer E; Phetsouphanh C; Hastak P; Hewavisenti RV; Joshi RV; Turner T; Cromer D; Sasson SC; Davenport MP; Khoury DS, 2026, Immunogenicity and vaccine effectiveness of COVID-19 vaccines in people on immunosuppressive therapies, http://dx.doi.org/10.64898/2026.09.16.26363194

Hogan AB; Wu SL; Toor J; Doohan P; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, 2022, Long Term Vaccination Strategies to Mitigate the Global Impact of SARS-CoV-2 Transmission: A Modelling Study, http://dx.doi.org/10.2139/ssrn.4135323

Koutsakos M; Reynaldi A; Lee WS; Nguyen J; Amarasena T; Taiaroa G; Kinsella P; Liew KC; Tran T; Kent H; Tan H-X; Rowntree L; Nguyen T; Thomas P; Kedzierska K; Petersen J; Rossjohn J; Williamson D; Khoury D; Davenport M; Kent S; Wheatley A; Juno J, 2022, Rapid Recall and de novo T Cell Responses During SARS-CoV-2 Breakthrough Infection, http://dx.doi.org/10.2139/ssrn.4311124

Aggarwal A; Stella A; Walker G; Akerman A; Milogiannakis V; Brilot F; Amatayakul-Chantler S; Roth N; Coppola G; Schofield P; Jackson J; Lenthall H; Mazigi O; Langley D; Lu Y; Forster C; McAllery S; Mathivanan V; Fitcher C; Hoppe AC; Munier CML; Jack H-M; Cromer D; Darley D; Matthews G; Christ D; Khoury D; Davenport M; Rawlinson W; Kelleher A; Turville S, 2022, SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern, http://dx.doi.org/10.21203/rs.3.rs-1207364/v1

Mehra S; Stadler E; Khoury D; McCaw JM; Flegg JA, 2021, Hypnozoite dynamics for Plasmodium vivax malaria: the epidemiological effects of radical cure, http://dx.doi.org/10.48550/arxiv.2107.00779

Cromer D; Steain M; Reynaldi A; Schlub TE; Wheatley AK; Juno JA; Kent SJ; Triccas JA; Khoury DS; Davenport MP, 2021, SARS-CoV-2 variants: levels of neutralisation required for protective immunity, http://dx.doi.org/10.1101/2021.08.11.21261876

Khoury DS; Cromer D; Reynaldi A; Schlub TE; Wheatley AK; Juno JA; Subbarao K; Kent SJ; Triccas JA; Davenport MP, 2021, What level of neutralising antibody protects from COVID-19?, http://dx.doi.org/10.1101/2021.03.09.21252641

Soon M; Lee HJ; Engel J; Straube J; Thomas B; Clarke L; Laohamonthonkul P; Pernold C; Haldar R; Williams C; Lansink L; Koufariotis R; Lakis V; Wood S; Chen X; James K; Lönnberg T; Lane S; Davenport M; Khoury D; Svensson V; Teichmann S; Haque A, 2019, Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4 ⁺ T cells, http://dx.doi.org/10.1101/675967

Cao P; Klonis N; Zaloumis S; Khoury DS; Cromer D; Davenport MP; Tilley L; Simpson JA; McCaw JM, 2017, A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection, http://dx.doi.org/10.48550/arxiv.1701.05302

Khoury DS; Steain M; Triccas JA; Sigal A; Davenport MP; Cromer D, A meta-analysis of Early Results to predict Vaccine efficacy against Omicron, http://dx.doi.org/10.1101/2021.12.13.21267748

Stadler E; Cromer D; Ogunlade S; Ongoiba A; Doumbo S; Kayentao K; Traore B; Crompton PD; Portugal S; Davenport MP; Khoury DS, A role for super-spreaders in carrying malaria parasites across the months-long dry season, http://dx.doi.org/10.1101/2022.04.28.22274398

Singanayagam A; Wagstaffe HR; Slater L; Fox-Sheehan P; Wu M-S; Mawer A; Preston-Jones H; Daly O; Low JM; Ramon RL; Hughes E; Zhou J; Badhan A; Guy J; Harris SA; Smith SP; Govender M; Laidlaw SM; Tipton T; Satti I; Yaden M; Ascough S; Sukhova K; Moshe M; McKenzie J; Siddiqui H; Ateere A; Nassanga B; Stiff F; Khoury DS; Reynaldi A; Davenport MP; Carroll M; Thwaites RS; Taylor GP; Barclay W; Bracchi M; McShane H; Chiu C; team TCS, Biomarkers of protection against controlled human SARS-CoV-2 Delta variant breakthrough infection, http://dx.doi.org/10.64898/2026.07.24.26358855

Khoury DS; Schlub TE; Cromer D; Steain M; Fong Y; Gilbert PB; Subbarao K; Triccas JA; Kent SJ; Davenport MP, Correlates of protection, thresholds of protection, and immunobridging in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.06.05.22275943

Stadler E; Chai KL; Schlub TE; Cromer D; Polizzotto MN; Kent SJ; Beecher C; White H; Turner T; Skoetz N; Estcourt L; McQuilten ZK; Wood EM; Khoury DS; Davenport MP, Determinants of passive antibody efficacy in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.03.21.22272672

Lee WS; Tan H-X; Reynaldi A; Esterbauer R; Koutsakos M; Nguyen J; Amarasena T; Kent HE; Aggarwal A; Turville SG; Taiaroa G; Kinsella P; Liew KC; Tran T; Williamson DA; Cromer D; Davenport MP; Kent SJ; Juno JA; Khoury DS; Wheatley AK, Durable reprogramming of neutralising antibody responses following breakthrough Omicron infection, http://dx.doi.org/10.1101/2023.02.19.23286159

Koutsakos M; Lee WS; Reynaldi A; Tan H-X; Gare G; Kinsella P; Liew KC; Williamson DA; Kent HE; Stadler E; Cromer D; Khoury DS; Wheatley AK; Juno JA; Davenport MP; Kent SJ, Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection, http://dx.doi.org/10.1101/2021.12.23.21268285

Hogan AB; Doohan P; Wu SL; Mesa DO; Toor J; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, Estimating long-term vaccine effectiveness against SARS-CoV-2 variants: a model-based approach, http://dx.doi.org/10.1101/2023.01.03.23284131

Stadler E; Csolle M; Mitchell A; Egilmezer E; Elias KM; Bailey BA; Cromer D; Turner T; Khoury DS; Davenport MP, Evidence for cross-reactivity and protection against Bundibugyo virus disease after heterologous vaccination: a systematic review and meta-analysis, http://dx.doi.org/10.64898/2026.09.14.26362805

Wheatley AK; Juno JA; Wang JJ; Selva KJ; Reynaldi A; Tan H-X; Lee WS; Wragg KM; Kelly HG; Esterbauer R; Davis SK; Kent HE; Mordant FL; Schlub TE; Gordon DL; Khoury DS; Subbarao K; Cromer D; Gordon TP; Chung AW; Davenport MP; Kent SJ, Evolution of immunity to SARS-CoV-2, http://dx.doi.org/10.1101/2020.09.09.20191205

Chung Y; Bailey BA; Bowden-Reid E; Csolle M; Docken SS; Jachno K; Khoury DS; McDonald S; Pattuwage L; White H; Zazryn T; Turner T; Davenport MP, Filovirus Evidence Maps: A community resource to identify and curate the published evidence on immunity and vaccination for BDBV, EBOV, MARV, and SUDV, http://dx.doi.org/10.64898/2026.05.22.26353826

Berry MT; Palmer MR; Khan SR; Bowden-Reid E; Egilmezer E; Smith MA; Bateson D; Canfell K; Davenport MP; Khoury DS, HPV binding antibodies as a correlate of protection, http://dx.doi.org/10.1101/2025.11.26.25341002

Hogan AB; Wu SL; Toor J; Mesa DO; Doohan P; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, Long term vaccination strategies to mitigate the impact of SARS-CoV-2 transmission: a modelling study, http://dx.doi.org/10.1101/2023.02.09.23285743

Stadler E; Burgess MT; Schlub TE; Chai KL; McQuilten ZK; Wood EM; Polizzotto MN; Kent SJ; Cromer D; Davenport MP; Khoury DS, Monoclonal antibody levels and protection from COVID-19, http://dx.doi.org/10.1101/2022.11.22.22282199

Goel RR; Painter MM; Apostolidis SA; Mathew D; Meng W; Rosenfeld AM; Lundgreen KA; Reynaldi A; Khoury DS; Pattekar A; Gouma S; Kuri-Cervantes L; Hicks P; Dysinger S; Hicks A; Sharma H; Herring S; Korte S; Baxter AE; Oldridge DA; Giles JR; Weirick ME; McAllister CM; Awofolaju M; Tanenbaum N; Drapeau EM; Dougherty J; Long S; D’Andrea K; Hamilton JT; McLaughlin M; Williams JC; Adamski S; Kuthuru O; Unit TUCP; Frank I; Betts MR; Vella LA; Grifoni A; Weiskopf D; Sette A; Hensley SE; Davenport MP; Bates P; Prak ETL; Greenplate AR; Wherry EJ, mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern, http://dx.doi.org/10.1101/2021.08.23.457229

Cromer D; Steain M; Reynaldi A; Schlub TE; Sasson SC; Kent SJ; Khoury DS; Davenport MP, Neutralising antibodies predict protection from severe COVID-19, http://dx.doi.org/10.1101/2022.06.09.22275942

Berry MT; MacIntyre CR; Cromer D; Hacker A; Davenport MP; Khoury DS, Optimal deployment of limited vaccine supplies to combat mpox, http://dx.doi.org/10.1101/2024.11.03.24316551

Ashley CL; Bloul M; Alca S; Smith L; Jin W; Khoury D; Counoupas C; Davenport M; Triccas JA; Steain M, Optimisation of a multiplexed, high throughput assay to measure neutralising antibodies against SARS-CoV-2 variants, http://dx.doi.org/10.1101/2024.09.01.610733

Cromer D; Reynaldi A; Hie A; Schlub TE; Juno JA; Wheatley AK; Kent SJ; Khoury DS; Davenport MP, Predicting COVID-19 booster immunogenicity against future SARS-CoV-2 variants and the benefits of vaccine updates, http://dx.doi.org/10.1101/2024.02.08.24302032

Khoury DS; Docken SS; Subbarao K; Kent SJ; Davenport MP; Cromer D, Predicting the efficacy of variant-modified COVID-19 vaccine boosters, http://dx.doi.org/10.1101/2022.08.25.22279237

Berry MT; Khan SR; Schlub TE; Notaras A; Kunasekaran M; Grulich AE; MacIntyre CR; Davenport MP; Khoury DS, Predicting vaccine effectiveness in Mpox, http://dx.doi.org/10.1101/2023.11.23.23298850

Hogan AB; Mitchell A; Stadler E; Chung Y; Reynaldi A; Elias KM; Docken S; Khoury DS; Schlub T; Davenport MP; Cromer D, Quantifying the association between neutralising antibodies and protection from RSV disease in infants and adults: A systematic review and meta-analysis, http://dx.doi.org/10.64898/2026.02.13.26346212

Koutsakos M; Reynaldi A; Lee WS; Nguyen J; Amarasena T; Taiaroa G; Kinsella P; Liew KC; Tran T; Kent HE; Tan H-X; Rowntree LC; Nguyen THO; Thomas PG; Kedzierska K; Petersen J; Rossjohn J; Williamson DA; Khoury D; Davenport MP; Kent SJ; Wheatley AK; Juno JA, Rapid recall and de novo T cell responses during SARS-CoV-2 breakthrough infection, http://dx.doi.org/10.1101/2022.12.19.521129

Cromer D; Reynaldi A; Steain M; Triccas JA; Davenport MP; Khoury DS, Relating in vitro neutralisation level and protection in the CVnCoV (CUREVAC) trial, http://dx.doi.org/10.1101/2021.06.29.21259504

Stadler E; Cromer D; Mehra S; Adekunle AI; Flegg JA; Anstey NM; Watson JA; Chu CS; Mueller I; Robinson LJ; Schlub TE; Davenport MP; Khoury DS, Risk of Plasmodium vivax recurrences follows a 30-70 rule and indicates relapse heterogeneity in the population, http://dx.doi.org/10.1101/2022.05.18.22275180

Williams CG; Moreira ML; Asatsuma T; Skinner OP; Lee HJ; Li S; Barrera I; Murray E; Soon MSF; Engel JA; Khoury DS; Asad S; Steiner TM; Joseph R; Alexandre Y; Mueller SN; Chen F; Haque A, Spatial transcriptomics maps molecular and cellular requirements for CD4+ T cell-dependent immunity to malaria, http://dx.doi.org/10.1101/2023.02.23.529309

Lansink LIM; Engel JA; Lee HJ; Soon MSF; Williams CG; SheelaNair A; Pernold CPS; Laohamonthonkul P; Akter J; Stoll T; Hill MM; Talman AM; Russell A; Lawniczak M; Davenport MP; Khoury DS; Haque A, Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites, http://dx.doi.org/10.1101/2021.08.18.456784

Skinner OP; Asad S; Moreira ML; Lee HJ; Williams CG; Ruan Z; Lim J; Kerr AS; Li S; Zhu C; Jin W; Steiner TM; Asatsuma T; Wanrooy BJ; Liu Z; Tong MZW; Soon MSF; Engel JA; Shobhana K; Uldrich AP; Khoury DS; Tuong ZK; King HW; Haque A, Temporally overlapping mechanisms diversify clonal B cell responses in vivo, http://dx.doi.org/10.1101/2024.12.17.628863

Hogan AB; Wu SL; Doohan P; Watson OJ; Winskill P; Charles G; Barnsley G; Riley EM; Khoury DS; Ferguson NM; Ghani AC, The value of vaccine booster doses to mitigate the global impact of the Omicron SARS-CoV-2 variant, http://dx.doi.org/10.1101/2022.01.17.22269222

Elias KM; Khan SR; Stadler E; Schlub TE; Cromer D; Polizzotto MN; Kent SJ; Turner T; Davenport MP; Khoury DS, Viral clearance as a surrogate of clinical efficacy for COVID-19 therapies in outpatients: A systematic review and meta-analysis, http://dx.doi.org/10.1101/2023.06.18.23291566

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